Agri-food industries must guarantee the safety of the produced foods through the application of the existing regulations, by correctly implementing quality control systems. In relation to the quality of drinking milk, it is extremely important to monitor the industrial treatments to which it is subjected to avoid the multiplication of spoilage and pathogenic microorganisms. Raw milk must undergo strict quality controls at the primary production level based on the knowledge of the main factors that influence their quality and microbiological safety: hygienic practices, health status of cows, frequency and moment of collection, storage temperature and time of transportation. To improve food safety and estimate food shelf life, predictive microbiology is a widely used tool for the estimation of microbial behavior as a function of intrinsic and extrinsic by using mathematical models. Throughout this chapter, a description of the current food quality management systems (FQMS) carried out by dairy industries will be provided by reflecting the current challenges, the guidelines, and available tools. A case study based on the application of predictive microbiology considering the importance of controlling certain factors in the primary production dairy chain will be developed.